Configuring Horizon
coollabsio/coolify
A skill your agent uses whenever the user mentions Horizon by name in a Laravel context.
A skill your agent uses when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands).
Install Pdb Database
$ npx skills add google-deepmind/science-skills --skill pdb-database -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install google-deepmind/science-skills pdb-database --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/pdb_database .claude/skills/pdb-database && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "pdb-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pdb_database into .claude/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/google-deepmind/science-skills/tree/main/skills/pdb_databaseType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add google-deepmind/science-skills --skill pdb-database -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install google-deepmind/science-skills pdb-database --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/pdb_database .agents/skills/pdb-database && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "pdb-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pdb_database into .agents/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add google-deepmind/science-skills --skill pdb-database -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install google-deepmind/science-skills pdb-database --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/pdb_database .cursor/skills/pdb-database && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "pdb-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pdb_database into .cursor/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/google-deepmind/science-skills.git --path skills/pdb_database--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add google-deepmind/science-skills --skill pdb-database -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install google-deepmind/science-skills pdb-database --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/pdb_database .gemini/skills/pdb-database && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "pdb-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pdb_database into .gemini/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install google-deepmind/science-skills pdb-databaseInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add google-deepmind/science-skills --skill pdb-database -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/pdb_database .github/skills/pdb-database && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "pdb-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pdb_database into .github/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add google-deepmind/science-skills --skill pdb-database -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install google-deepmind/science-skills pdb-database --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/pdb_database .opencode/skills/pdb-database && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "pdb-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pdb_database into .opencode/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
pdb-database- GitHub stars
- 3.2k
- Used in
- 2 other repos
- Token cost
- ~2.2k tokens
- SKILL.md length
- 622 words
- Files
- 6 (incl. scripts, references)
- Skills in repo
- 40
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
A skill your agent uses when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands).
- Works in 2 steps: uv: Read the uv skill and follow its… → User Notification: If…
- You want to search for
- SKILL.md covers Prerequisites, Core Rules, Attribute-based search workflow and Similarity-based search workflow, plus 3 more sections
- Runs Python scripts from its folder; calls uv
What it does
Pdb Database is an agent skill from google-deepmind/science-skills. Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes. Also use to get metadata about biomolecular structure experiments.
Its SKILL.md is about 2.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files, including scripts and reference files (for example `scripts/download_coordinate_files.py`, `scripts/fetch_pdb_metadata.py` and `scripts/fetch_schema.py`).
It sits in Backend & APIs. The repository describes itself as: GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other… The licence is Apache-2.0.
When your agent uses it
- You want to search for
- Download experimentally-determined 3D structures for biomolecules (proteins
- Get metadata about biomolecular structure experiments
Example prompts
- “/pdb-database”
Requirements
- Python 3
Workflow steps
2 steps, taken from the first numbered list in SKILL.md.
- uv: Read the uv skill and follow its Setup instructions to ensure
- User Notification: If .licenses/pdb_database_LICENSE.txt does not
What it can do on your machine
Read from SKILL.md and the folder at commit 6883275. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 4 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
uv
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
rcsb.orgsearch.rcsb.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Pdb Database loads about 2.2k tokens when it runs, and up to ~2.4k if it reads all its reference files. Until then it costs about 80 tokens; SKILL.md has 622 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
The full file from google-deepmind/science-skills at commit 6883275, republished under its Apache-2.0 licence (© google-deepmind). 622 words, ~2,223 tokens.
Download SKILL.mdSave it as
.claude/skills/pdb-database/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.- name
- pdb-database
- description
- Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes. Also use to get metadata about biomolecular structure experiments.
RCSB Protein Data Bank skill
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- User Notification: If .licenses/pdb_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.rcsb.org/pages/usage-policy, then (2) create the file recording the notification text and timestamp.
Core Rules
- Always prefer to use the provided scripts. Only as a last resort use
curl,urllib, raw HTTP requests, or any other method to access PDB APIs. The scripts automatically enforce required rate limits. - Always redirect output to a file. Parse output with e.g.
jq,grep, or a short Python snippet. Do NOT print large API responses to stdout to avoid truncation. - Notification: If this skill is used, ensure this is mentioned in the output.
- Explain your queries On completing a task that used PDB JSON/GraphQL queries, explain in clear language what your query did so the user can correct any bad assumptions.
Attribute-based search workflow
Fetch the relevant schema to discover searchable attribute names. For structure attributes:
uv run scripts/fetch_schema.py --api search_structure --output schema_structure.txtFor chemical attributes:uv run scripts/fetch_schema.py --api search_chemical --output schema_chemical.txtGrep the schema to find relevant attributes. Grep one keyword at a time and examine many lines — there are lots of similar attributes and you must choose the best match for the user's intent.
Compose and run a JSON search query using the discovered attributes:
uv run scripts/search_pdb.py --query '<JSON>' --return_type <RETURN_TYPE> --output results.jsonPass the--count_onlyflag to get just the number of matching entries.
For step 2: some basic PDB concepts (helpful for attribute choice)
- Entity: A unique molecule found in a structure.
- Instance / Chain: A particular copy of an entity. E.g. if a structure contains two protein chains with the same sequence, they are the same entity but different instances / chains.
- Assembly: A biologically relevant collection of instances / chains. This may be the same as the deposited structure, a subset, or multiple copies.
- Label vs Auth: Polymer instances get letter labels ("A", "B", "AA") and their monomers are numbered. There are author-assigned ("auth") and PDB-internal ("label") schemes. The label scheme is more consistent and is always used in scripts and APIs. However, users and papers may refer to the author scheme (clarify which scheme is being used if necessary).
- Chemical component: A small molecule / monomer, with an ID matching
[A-Z]{1,3} - Primary citation: The main publication about a structure. Prefer
primary_citationattributes overcitationattributes. - Resolution: Frequently used measure of structure quality (lower is
better). Usually prefer
rcsb_entry_info.resolution_combined, which accounts for different experimental methods.
Show full SKILL.md (185 more words)Show less
For step 3: Example queries
# Non-human proteins published in Nature, newest first
uv run scripts/search_pdb.py --query '{ "type": "group", "logical_operator": "and", "nodes": [ { "type": "terminal", "service": "text", "parameters": { "operator": "exact_match", "negation": true, "value": "Homo sapiens", "attribute": "rcsb_entity_source_organism.taxonomy_lineage.name" } }, { "type": "terminal", "service": "text", "parameters": { "operator": "exact_match", "value": "Nature", "attribute": "rcsb_primary_citation.rcsb_journal_abbrev" } } ] }' --return_type entry --sort_by rcsb_accession_info.initial_release_date --sort_direction desc --page_start 0 --rows 100 --output results.json# Structures containing the chemical component CA (Ca2+ ion)
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "text_chem", "parameters": { "operator": "exact_match", "value": "CA", "attribute": "rcsb_chem_comp_container_identifiers.comp_id" } }' --return_type entry --output results.json# Number of entries with disulfide bonds
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "text", "parameters": { "operator": "exact_match", "value": "disulfide bridge", "attribute": "rcsb_polymer_struct_conn.connect_type" } }' --return_type entry --count-only --output count.jsonCommon operators: exact_match, equals, exists, contains_phrase,
contains_words, in, greater, less
Similarity-based search workflow
Similarity searches do not require a schema fetch. Basic examples:
# Sequence similarity
uv run scripts/search_pdb.py --query '{ "query": { "type": "terminal", "service": "sequence", "parameters": { "evalue_cutoff": 1, "identity_cutoff": 0.9, "sequence_type": "protein", "value": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQ" } }, "request_options": { "scoring_strategy": "sequence" } }' --return_type polymer_entity --output results.json# Structure similarity
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "structure", "parameters": { "value": {"entry_id": "6LU7", "asym_id": "A"}, "number_of_candidates": 2000 } }' --return_type polymer_entity --output results.json# Sequence motif match
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "seqmotif", "parameters": { "value": "C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H.", "pattern_type": "prosite", "sequence_type": "protein" } }' --return_type polymer_entity --output results.json# Chemical descriptor match
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "chemical", "parameters": { "value": "InChI=1S/C8H9NO2/c1-6(10)9-7-2-4-8(11)5-3-7/h2-5,11H,1H3,(H,9,10)", "type": "descriptor", "descriptor_type": "InChI", "match_type": "graph-strict" } }' --return_type mol_definition --output results.jsonSee https://search.rcsb.org/#search-services for more details.
Full text search workflow
Searches all text associated with an entry. Example:
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "full_text", "parameters": { "value": "isopeptide + ( collagen | fibrinogen )" } }' --return_type entry --output results.jsonImportant: use
full_textsearch as a last resort when there's no more precise attribute search available. Consider using thestruct.titleorrcsb_pubmed_abstract_textattributes instead.
File download workflow
To download full PDB entries, use the download_coordinate_files.py script. Use
this when you need access to atomic coordinates, when asked for a pdb / mmcif
file, or when non-specifically asked to fetch a PDB code. Example:
uv run scripts/download_coordinate_files.py --ids "4HHB,6BEA" --format "mmcif" --output_dir <OUTPUT_DIR>Metadata query workflow
This flow is significantly more efficient than downloading full coordinate files when you only need a few pieces of metadata about each entry / entity.
Fetch the schema for the relevant object type. E.g.
uv run scripts/fetch_schema.py --api data_entry --output schema_entry.txtGrep the schema for relevant fields (one keyword at a time, many lines).
Compose and run a GraphQL metadata query:
uv run scripts/fetch_pdb_metadata.py --query '<GraphQL>' --output results.json
For step 3: Example queries
# Fetch structure titles and experimental methods
uv run scripts/fetch_pdb_metadata.py --query '{ entries(entry_ids: ["1STP", "2JEF", "1CDG"]) { rcsb_id struct { title } exptl { method } } }' --output results.json# Fetch polymer entity taxonomy and cluster membership
uv run scripts/fetch_pdb_metadata.py --query '{ polymer_entities(entity_ids:["2CPK_1","3WHM_1","2D5Z_1"]) { rcsb_id rcsb_entity_source_organism { ncbi_taxonomy_id ncbi_scientific_name } rcsb_cluster_membership { cluster_id identity } } }' --output results.json# Fetch polymer entity external sequence database accessions
uv run scripts/fetch_pdb_metadata.py --query '{ entries(entry_ids:["7NHM", "5L2G"]){ polymer_entities { rcsb_id rcsb_polymer_entity_container_identifiers { reference_sequence_identifiers { database_accession database_name } } } } }' --output results.json© google-deepmind, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 5 other files (scripts, references) in skills/pdb_database of google-deepmind/science-skills.
- SKILL.md
- references/citation.bib
- scripts/download_coordinate_files.py
- scripts/fetch_pdb_metadata.py
- scripts/fetch_schema.py
- scripts/search_pdb.py
Open the folder on GitHubat commit 6883275
Used in 2 other repositories
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in google-deepmind/science-skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Pdb Database next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Pdb Database this skillgoogle-deepmind/science-skills | 3.2k | 2 repos | ~2.2k | Automated safety check: Pass | Apache-2.0 | |
| Configuring Horizoncoollabsio/coolify | 63k | 4 repos | ~898 | Automated safety check: Pass | MIT | |
| Nestjs Best Practicesrolling-scopes/rsschool-app | 10k | 6 repos | ~1.2k | Automated safety check: Pass | MIT | |
| Sub2API AdminWei-Shaw/sub2api | 43k | 1 repos | ~717 | Automated safety check: Pass | LGPL-3.0 | |
| Firecrawl Build Onboardingfirecrawl/firecrawl | 190k | 1 repos | ~1.4k | Automated safety check: Notes | ISC | |
| Obsidian BasesAtmosphere/atmosphere | 3.8k | 22 repos | ~3.2k | Automated safety check: Pass | Apache-2.0 |
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Related
Categories
Questions about Pdb Database
What does Pdb Database do?
A skill your agent uses when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Pdb Database is an agent skill from google-deepmind/science-skills. Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands).
When should I use Pdb Database?
Pdb Database fits situations like: you want to search for; download experimentally-determined 3D structures for biomolecules (proteins; get metadata about biomolecular structure experiments.
How do I install Pdb Database in Claude Code?
Run `npx skills add google-deepmind/science-skills --skill pdb-database -a claude-code`. Or copy the skill folder (skills/pdb_database in google-deepmind/science-skills) into .claude/skills/pdb-database in your project. Claude Code loads it when a task matches its description.
How do I install Pdb Database in Codex?
Run `npx skills add google-deepmind/science-skills --skill pdb-database -a codex`. Or copy the skill folder (skills/pdb_database in google-deepmind/science-skills) into .agents/skills/pdb-database in your project. Codex loads it when a task matches its description.
Can I use Pdb Database in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add google-deepmind/science-skills --skill pdb-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pdb-database, .gemini/skills/pdb-database, .github/skills/pdb-database and .opencode/skills/pdb-database in your project.
What does Pdb Database need to run?
Going by SKILL.md and its folder, Pdb Database needs Python for the scripts in its folder and the command-line tools its instructions call (uv). Our summary lists: Python 3.
Does Pdb Database access the network?
SKILL.md names 2 domains. As links in the text: rcsb.org and search.rcsb.org. This is read from the text; nothing was executed.
Is Pdb Database safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Pdb Database use?
Pdb Database is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Pdb Database use?
About 2.2k tokens (SKILL.md is roughly 8.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 220 tokens, read only when the agent opens those files.
What are the alternatives to Pdb Database?
Skills that share tags, products or a category with Pdb Database: Configuring Horizon (coollabsio/coolify, 63k stars), Nestjs Best Practices (rolling-scopes/rsschool-app, 10k stars), Sub2API Admin (Wei-Shaw/sub2api, 43k stars) and Firecrawl Build Onboarding (firecrawl/firecrawl, 190k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Pdb Database?
google-deepmind (a GitHub organization) maintains it in google-deepmind/science-skills, which has 3,220 GitHub stars. The repository holds 40 skills in this directory. The repository was last updated on September 15, 2026.
Source: google-deepmind/science-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.